[English] 日本語
Yorodumi
- PDB-2h9h: An episulfide cation (thiiranium ring) trapped in the active site... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h9h
TitleAn episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors
Components
  • Hepatitis A virus protease 3C
  • Three residue peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / METHYLKETONE / EPISULFIDE / HYDROLASE-HYDRLASE INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-acetyl-L-leucyl-L-alanyl-N-[(1S)-4-(dimethylamino)-1-(fluoroacetyl)-4-oxobutyl]-L-alaninamide / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsYin, J. / Cherney, M.M. / Bergmann, E.M. / James, M.N.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: An Episulfide Cation (Thiiranium Ring) Trapped in the Active Site of HAV 3C Proteinase Inactivated by Peptide-based Ketone Inhibitors.
Authors: Yin, J. / Cherney, M.M. / Bergmann, E.M. / Zhang, J. / Huitema, C. / Pettersson, H. / Eltis, L.D. / Vederas, J.C. / James, M.N.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Dual modes of modification of Hepatitis A virus 3C protease by a Serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site
Authors: Yin, J. / Bergmann, E.M. / Cherney, M.M. / Lall, M.S. / Jain, R.P. / Vederas, J.C. / James, M.N.G.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatitis A virus protease 3C
I: Three residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9843
Polymers23,7602
Non-polymers2231
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.672, 56.055, 80.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer

-
Components

#1: Protein Hepatitis A virus protease 3C


Mass: 23288.844 Da / Num. of mol.: 1 / Fragment: 3C PROTEINASE, RESIDUES 1520-1731 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Gene: 3C / Plasmid: pHAV-3CEX / Production host: Escherichia coli (E. coli) / Strain (production host): D1210
References: UniProt: P06441, UniProt: P08617*PLUS, picornain 3C
#2: Protein/peptide Three residue peptide


Type: Peptide-like / Class: Inhibitor / Mass: 471.567 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-acetyl-L-leucyl-L-alanyl-N-[(1S)-4-(dimethylamino)-1-(fluoroacetyl)-4-oxobutyl]-L-alaninamide
#3: Chemical ChemComp-BBL / N-[(BENZYLOXY)CARBONYL]-L-ALANINE / N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE


Mass: 223.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 297 K / pH: 7.5
Details: 2.5% PEG 8000, 1.5% Glycerol, 10mM tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2004
RadiationMonochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 1.35→26.49 Å / Num. obs: 36919 / % possible obs: 81.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.6 / % possible all: 22.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A4O

2a4o


Resolution: 1.39→26.49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.599 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1838 5.1 %RANDOM
Rwork0.181 ---
obs0.182 34294 86.7 %-
all-34342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.55 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.39→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 16 263 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9712313
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0085215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31524.92869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.304157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89941096
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90561725
X-RAY DIFFRACTIONr_scbond_it3.988692
X-RAY DIFFRACTIONr_scangle_it5.82910588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 60 -
Rwork0.329 1267 -
obs--43.51 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more